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**phytools**: Phylogenetic Tools for Comparative Biology (and Other Things)**densityTree**: Plots a posterior sample of trees

# Plots a posterior sample of trees

### Description

Functions plots a posterior sample of trees, including with mapped discrete characters.

`make.transparent`

is used internally and converts a color to transparent with a certain user-specified `alpha`

level.

### Usage

1 2 3 | ```
densityTree(trees, colors="blue", alpha=NULL, method="plotTree", fix.depth=FALSE,
use.edge.length=TRUE, compute.consensus=FALSE, ...)
make.transparent(color, alpha)
``` |

### Arguments

`trees` |
an object of class |

`colors` |
a color or a named vector of colors in which names correspond to mapped states in an object of class |

`alpha` |
transparency level for plotted trees which is passed to internally used function, |

`method` |
plotting method to be used internally. Can be |

`fix.depth` |
logical value indicating whether or not to plot trees with a fixed depth or to permit plotted trees to have different depths. |

`use.edge.length` |
logical value indicating whether to use the edge lengths of the input tree. Defaults to |

`compute.consensus` |
logical value indicating whether or not to use the tip order from a consensus tree. (Defaults to |

`...` |
arguments to be passed to |

`color` |
in |

### Value

Function creates a plot.

### Author(s)

Liam Revell liam.revell@umb.edu

### References

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). *Methods Ecol. Evol.*, **3**, 217-223.

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker. Vote for new features on Trello.

- add.arrow: Add an arrow pointing to a tip or node on the tree
- add.color.bar: Add color bar to a plot
- add.everywhere: Add tip to all edges in a tree
- add.random: Add tips at random to the tree
- add.simmap.legend: Add legend to stochastically mapped tree
- add.species.to.genus: Add species to genus on a phylogeny or bind simulated species...
- allFurcTrees: Generate all bi- and multifurcating unrooted trees
- anc.Bayes: Bayesian ancestral character estimation
- anc.ML: Ancestral character estimation using likelihood
- ancThresh: Ancestral character estimation under the threshold model...
- anc.trend: Ancestral character estimation with a trend
- anoletree: Phylogeny of Greater Antillean anole ecomorph species with...
- applyBranchLengths: Applies the branch lengths of a reference tree to a target
- as.multiPhylo: Conversion to object of class '"multiPhylo"'
- averageTree: Compute an average tree from a set of trees and related...
- ave.rates: Average the posterior rates
- bind.tip: Attaches a new tip to a tree
- bind.tree.simmap: Attaches a new tip to a tree
- bmPlot: Simulates and visualizes discrete-time Brownian evolution on...
- branching.diffusion: Animation of branching random diffusion
- brownie.lite: Likelihood test for rate variation in a continuous trait
- brownieREML: REML version of brownie.lite
- cladelabels: Add labels to subtrees of a plotted phylogeny
- collapse.to.star: Collapse a subtree to a star phylogeny
- collapseTree: Interactive tree visualizer
- consensus.edges: Compute consensus edges for a tree under some criterion
- contMap: Map continuous trait evolution on the tree
- cophylo: Creates a co-phylogenetic plot
- countSimmap: Counts the number of character changes on a SIMMAP style tree...
- densityMap: Plot posterior density of stochastic mapping on a tree
- densityTree: Plots a posterior sample of trees
- describe.simmap: Summarizes a stochastic mapped tree or set of trees
- di2multi.simmap: Collapse branches of zero length to polytomy in stochastic...
- dotTree: Creates a phylogenetic dot plot
- drop.clade: Drop a clade from a tree
- drop.leaves: Drop all the leaves (tips) from a tree
- drop.tip.contMap: Drop tip or tips from an object of class "contMap" or...
- drop.tip.simmap: Drop tips or extract clade from tree with mapped discrete...
- edgeProbs: Compute the relative frequencies of state changes along edges
- estDiversity: Estimate diversity at each node of the tree
- evol.rate.mcmc: Bayesian MCMC method for identifying exceptional phenotypic...
- evol.vcv: Likelihood test for variation in the evolutionary VCV matrix
- evolvcv.lite: Likelihood test for a shift in the evolutionary correlation...
- exhaustiveMP: Exhaustive and branch & bound MP optimization
- expm: Matrix exponential
- export.as.xml: Export trees & data in XML format
- fancyTree: Plots special types of phylogenetic trees
- fastAnc: Fast estimation of ML ancestral states
- fastBM: Fast Brownian simulation
- fastMRCA: Get the MRCA (or height above the root of the MRCA) of a pair...
- findMRCA: Get the MRCA of a set of taxa
- fitBayes: Evolutionary model fitting with intraspecific variability...
- fitDiversityModel: Fit diversity-dependent phenotypic evolution model
- fitMk: Fits Mk model
- fitPagel: Function to test for correlated evolution of binary traits
- gammatest: Gamma test of Pybus & Harvey (2000)
- genSeq: Simulate a DNA alignment on the tree under a model
- getCladesofSize: Get all subtrees larger than or equal to a specified size
- getDescendants: Get descendant node numbers
- getExtant: Returns a list of the extant or extinct lineages in a tree...
- getSisters: Get the sister node number, label, or set of nodes for a node...
- getStates: Get the states at nodes or tips from a mapped tree
- ladderize.simmap: Ladderize a tree with a mapped discrete character
- lambda.transform: Lambda transformation of matrix
- likMlambda: Likelihood for joint lambda
- locate.fossil: Locate a fossil lineage in a tree using continuous characters
- locate.yeti: Locate a cryptic, recently extinct, or missing taxon on a...
- ls.tree: Least squares branch lengths for a given tree
- ltt: Creates lineage-through-time plot (including extinct...
- ltt95: Creates a (1-alpha)-percent CI for a set of LTTs
- make.era.map: Create "era" map on a phylogenetic tree
- make.simmap: Simulate stochastic character maps on a phylogenetic tree or...
- map.overlap: Proportional overlap between two mapped character histories...
- mapped.states: Returns a vector, matrix, or list of the mapped states on a...
- map.to.singleton: Converts a mapped tree to a tree with singleton nodes
- markChanges: Add marked changes to a plotted tree with mapped discrete...
- matchNodes: Matches nodes between two trees
- mergeMappedStates: Merge two or more mapped states into one state
- midpoint.root: Midpoint root a phylogeny
- minRotate: Rotates all nodes of the tree to minimize the difference in...
- minSplit: Finding the minimum (median) split in the posterior sample
- mrp.supertree: Matrix representation parsimony supertree estimation
- multiC: Returns a list with phylogenetic VCV matrix for each mapped...
- multi.mantel: Multiple matrix regression (partial Mantel test)
- multiRF: Computes Robinson-Foulds distance between a set of trees
- nodeHeights: Compute the heights above the root of each node
- nodelabels.cophylo: Add labels to a plotted "cophylo" object
- optim.phylo.ls: Phylogeny inference using the least squares method
- orderMappedEdge: Order the columns of mapped.edge to match across trees
- paintSubTree: Paint sub-trees with a discrete character
- paste.tree: Paste two trees together
- pbtree: Simulate pure-birth or birth-death stochastic tree or trees
- pgls.Ives: Phylogenetic regression with intraspecific sampling error
- phenogram: Plot phenogram (traitgram)
- phylANOVA: Phylogenetic ANOVA and post-hoc tests
- phyl.cca: Phylogenetic canonical correlation analysis
- phyloDesign: Compute design matrix for least squares analyses
- phylo.heatmap: Creates a phylogenetic heat map
- phylomorphospace: Creates phylomorphospace plot
- phylomorphospace3d: Creates tree-dimensional phylomorphospace plot
- phylosig: Compute phylogenetic signal with two methods
- phylo.toBackbone: Converts tree to backbone or vice versa
- phylo.to.map: Plot tree with tips linked to geographic coordinates
- phyl.pairedttest: Phylogenetic paired t-test
- phyl.pca: Phylogenetic principal components analysis
- phyl.resid: Phylogenetic size-correction via GLS regression
- phyl.RMA: Phylogenetic reduced major axis (RMA) regression
- phyl.vcv: Compute evolutionary VCV matrix for a tree & dataset
- phytools-package: phytools: Phylogenetic Tools for comparative biology (and...
- plot.backbonePhylo: Plots backbone tree with triangles as clades
- plotBranchbyTrait: Plot branch colors by a quantitative trait or value
- plotSimmap: Plot stochastic character mapped tree
- plotThresh: Tree plotting with posterior probabilities of ancestral...
- plotTree: Plots rooted phylogenetic tree
- plotTree.wBars: Plot a tree with bars at the tips
- posterior.evolrate: Analysis of the posterior sample from evol.rate.mcmc
- print.backbonePhylo: Print method for backbone phylogeny
- ratebystate: Method for investigating the rate of one trait as a function...
- rateshift: Find the temporal position of one or more rate shifts
- read.newick: Robust Newick style tree reader
- read.simmap: Read SIMMAP style trees from file
- reorder.backbonePhylo: Reorders a backbone phylogeny
- reorderSimmap: Reorder edges of a simmap tree
- rep.phylo: Replicate a tree or set of trees
- reroot: Re-root a tree along an edge
- rerootingMethod: Get marginal ancestral state reconstructions by re-rooting
- rescaleSimmap: Rescale SIMMAP style tree
- rotateNodes: Rotates a node or set of nodes in a phylogenetic tree
- roundBranches: Rounds the branch lengths of a tree
- roundPhylogram: Plot a round phylogram
- rstate: Pick a random state according to a vector of probabilities
- sampleFrom: Sample from a set of distributions
- setMap: Set color map for objects of class '"contMap"' or...
- sim.corrs: Multivariate Brownian simulation with multiple correlations...
- sim.history: Simulate stochastic character history under some model
- sim.ratebystate: Conduct simulation of state dependent rate variation
- sim.rates: Brownian simulation with multiple evolutionary rates
- skewers: Matrix comparison using the method of random skewers
- splitEdgeColor: Split edge colors when descendant edges have different mapped...
- splitplotTree: Plots a phylogeny in two columns
- splitTree: Split tree at a point
- starTree: Create star phylogeny
- strahlerNumber: Computes Strahler number for trees and nodes
- threshBayes: Threshold model using Bayesian MCMC
- threshDIC: Deviance Information Criterion from the threshold model
- threshState: Computes value for a threshold character from a liability and...
- to.matrix: Convert a character vector to a binary matrix
- treeSlice: Slices the tree at a particular point and returns all...
- untangle: Attempts to untangle crossing branches for plotting
- vcvPhylo: Calculates cophenetic (i.e., phylogenetic VCV) matrix
- writeAncestors: Write a tree to file with ancestral states and (optionally)...
- writeNexus: Write a tree to file in Nexus format
- write.simmap: Write a stochastic character mapped tree to file